scholarly journals Non-coding RNAs: New therapeutic targets and opportunities for hepatocellular carcinoma

2016 ◽  
Vol 2 (1) ◽  
pp. 5
Author(s):  
Yu Cuiyun ◽  
Qian Ning ◽  
Zhi-Ping Li ◽  
Wen Huang ◽  
Jia Yu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Open Reading Frame ◽  
Regulation Mechanism ◽  
Biological Processes ◽  
Biological Functions ◽  
Protein Coding ◽  
Reading Frame ◽  
Rna Molecules ◽  
Non Coding Rnas ◽  
Diagnosis Therapy

<p align="left">Non-coding RNAs (ncRNA) are RNA molecules without protein coding functions owing to the lack of an open reading frame (ORF). Based on the length, ncRNAs can be divided into long and short ncRNAs; short ncRNAs include miRNAs and piRNAs. Hepatocellular carcinoma (HCC) is among the most frequent forms of cancer worldwide and its incidence is increasing rapidly. Studies have found that ncRNAs are likely to play a crucial role in a variety of biological processes including the pathogenesis and progression of HCC. In this review, we summarized the regulation mechanism and biological functions of ncRNAs in HCC with respect to its application in HCC diagnosis, therapy and prognosis.</p>

scholarly journals Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

2020 ◽  
Vol 21 (10) ◽  
pp. 3711
Author(s):  
Melina J. Sedano ◽  
Alana L. Harrison ◽  
Mina Zilaie ◽  
Chandrima Das ◽  
Ramesh Choudhari ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Patterns ◽  
Biological Significance ◽  
Rna Seq ◽  
Biological Functions ◽  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

scholarly journals Translational products encoded by novel ORFs may form protein-like structures and have biological functions

2019 ◽  
Author(s):  
Chaitanya Erady ◽  
David Chong ◽  
Narendra Meena ◽  
Shraddha Puntambekar ◽  
Ruchi Chauhan ◽  
...  
Keyword(s):  
Systematic Study ◽  
Strong Evidence ◽  
Open Reading Frame ◽  
Biological Role ◽  
Biological Functions ◽  
Protein Coding ◽  
Reading Frame ◽  
Coding Regions ◽  
Disease States ◽  
Genomic Regions

AbstractTranslation products encoded by non canonical or novel open reading frame (ORF) genomic regions are generally considered too small to play any significant biological role, and dismissed as inconsequential. In this study, we show that mutations mapping to novel ORFs have significantly higher pathogenicity scores than mutations in protein-coding regions. Importantly, novel ORFs can translate into protein-like structures with putative independent biological functions that can be of relevance in disease states, including cancer. We thus provide strong evidence to support the systematic study of novel ORFs to gain new insights into normal biological and disease processes.One Sentence SummaryNon coding regions may encode protein-like products that are important to understand diseases.

scholarly journals MCM3AP-AS1: An Indispensable Cancer-Related LncRNA

2021 ◽  
Vol 9 ◽  
Author(s):  
Xiao Yu ◽  
Qingyuan Zheng ◽  
Qiyao Zhang ◽  
Shuijun Zhang ◽  
Yuting He ◽  
...  
Keyword(s):  
Cancer Diagnosis ◽  
Biological Function ◽  
Clinical Applications ◽  
Regulatory Mechanisms ◽  
Biological Functions ◽  
Tumor Node Metastasis ◽  
Protein Coding ◽  
Rna Molecules ◽  
Node Metastasis ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are a class of RNA molecules with transcripts longer than 200 nucleotides that have no protein-coding ability. MCM3AP-AS1, a novel lncRNA, is aberrantly expressed in human cancers. It is significantly associated with many clinical characteristics, such as tumor size, tumor-node-metastasis (TNM) stage, and pathological grade. Additionally, it considerably promotes or suppresses tumor progression by controlling the biological functions of cells. MCM3AP-AS1 is a promising biomarker for cancer diagnosis, prognosis evaluation, and treatment. In this review, we briefly summarized the published studies on the expression, biological function, and regulatory mechanisms of MCM3AP-AS1. We also discussed the clinical applications of MCM3AP-AS1 as a biomarker.

scholarly journals The function of non-coding RNAs in idiopathic pulmonary fibrosis

Open Medicine ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. 481-490
Author(s):  
Hui Zhang ◽  
Miao Song ◽  
Jianing Guo ◽  
Junbing Ma ◽  
Min Qiu ◽  
...  
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Poor Prognosis ◽  
Biological Functions ◽  
Protein Coding ◽  
Ribonucleic Acids ◽  
Rna Molecules ◽  
Evolutionarily Conserved ◽  
Non Coding Rnas ◽  
Regulate Protein

Abstract Non-coding ribonucleic acids (ncRNAs) are a diverse group of RNA molecules that are mostly not translated into proteins after transcription, including long non-coding RNAs (lncRNAs) with longer than 200 nucleotides non-coding transcripts and microRNAs (miRNAs) which are only 18–22 nucleotides. As families of evolutionarily conserved ncRNAs, lncRNAs activate and repress genes via a variety of mechanisms at both transcriptional and translational levels, whereas miRNAs regulate protein-coding gene expression mainly through mRNA silencing. ncRNAs are widely involved in biological functions, such as proliferation, differentiation, migration, angiogenesis, and apoptosis. Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with a poor prognosis. The etiology of IPF is still unclear. Increasing evidence shows the close correlations between the development of IPF and aberrant expressions of ncRNAs than thought previously. In this study, we provide an overview of ncRNAs participated in pathobiology of IPF, seeking the early diagnosis biomarker and aiming for potential therapeutic applications for IPF.

scholarly journals The Role of Extracellular Vesicles as Shuttles of RNA and Their Clinical Significance as Biomarkers in Hepatocellular Carcinoma

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 902
Author(s):  
Eva Costanzi ◽  
Carolina Simioni ◽  
Gabriele Varano ◽  
Cinzia Brenna ◽  
Ilaria Conti ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Extracellular Vesicles ◽  
Tumor Metastasis ◽  
Biological Processes ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Donor Cells ◽  
Relevant Role

Extracellular vesicles (EVs) have attracted interest as mediators of intercellular communication following the discovery that EVs contain RNA molecules, including non-coding RNA (ncRNA). Growing evidence for the enrichment of peculiar RNA species in specific EV subtypes has been demonstrated. ncRNAs, transferred from donor cells to recipient cells, confer to EVs the feature to regulate the expression of genes involved in differentiation, proliferation, apoptosis, and other biological processes. These multiple actions require accuracy in the isolation of RNA content from EVs and the methodologies used play a relevant role. In liver, EVs play a crucial role in regulating cell–cell communications and several pathophysiological events in the heterogeneous liver class of cells via horizontal transfer of their cargo. This review aims to discuss the rising role of EVs and their ncRNAs content in regulating specific aspects of hepatocellular carcinoma development, including tumorigenesis, angiogenesis, and tumor metastasis. We analyze the progress in EV-ncRNAs’ potential clinical applications as important diagnostic and prognostic biomarkers for liver conditions.

scholarly journals Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
T. M. Porter ◽  
M. Hajibabaei
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Dna Barcoding ◽  
Profile Analysis ◽  
Hidden Markov ◽  
Open Reading Frame ◽  
Protein Coding ◽  
Reading Frame ◽  
Frame Length ◽  
Open Reading Frame Length

Abstract Background Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes. Results Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place. Conclusions Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.

scholarly journals Promising Advances in LINC01116 Related to Cancer

2021 ◽  
Vol 9 ◽  
Author(s):  
Yating Xu ◽  
Xiao Yu ◽  
Menggang Zhang ◽  
Qingyuan Zheng ◽  
Zongzong Sun ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gastric Cancer ◽  
Lung Cancer ◽  
Cancer Colorectal ◽  
Malignant Tumors ◽  
Biological Processes ◽  
Aberrant Expression ◽  
Protein Coding ◽  
Future Studies ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are RNAs with a length of no less than 200 nucleotides that are not translated into proteins. Accumulating evidence indicates that lncRNAs are pivotal regulators of biological processes in several diseases, particularly in several malignant tumors. Long intergenic non-protein coding RNA 1116 (LINC01116) is a lncRNA, whose aberrant expression is correlated with a variety of cancers, including lung cancer, gastric cancer, colorectal cancer, glioma, and osteosarcoma. LINC01116 plays a crucial role in facilitating cell proliferation, invasion, migration, and apoptosis. In addition, numerous studies have recently suggested that LINC01116 has emerged as a novel biomarker for prognosis and therapy in malignant tumors. Consequently, we summarize the clinical significance of LINC01116 associated with biological processes in various tumors and provide a hopeful orientation to guide clinical treatment of various cancers in future studies.

scholarly journals Role of Main RNA Methylation in Hepatocellular Carcinoma: N6-Methyladenosine, 5-Methylcytosine, and N1-Methyladenosine

2021 ◽  
Vol 9 ◽  
Author(s):  
Yating Xu ◽  
Menggang Zhang ◽  
Qiyao Zhang ◽  
Xiao Yu ◽  
Zongzong Sun ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cellular Differentiation ◽  
Molecular Mechanisms ◽  
Gene Sequence ◽  
Epigenetic Modification ◽  
Biological Processes ◽  
Biological Functions ◽  
Rna Detection ◽  
Rna Methylation

RNA methylation is considered a significant epigenetic modification, a process that does not alter gene sequence but may play a necessary role in multiple biological processes, such as gene expression, genome editing, and cellular differentiation. With advances in RNA detection, various forms of RNA methylation can be found, including N6-methyladenosine (m6A), N1-methyladenosine (m1A), and 5-methylcytosine (m5C). Emerging reports confirm that dysregulation of RNA methylation gives rise to a variety of human diseases, particularly hepatocellular carcinoma. We will summarize essential regulators of RNA methylation and biological functions of these modifications in coding and noncoding RNAs. In conclusion, we highlight complex molecular mechanisms of m6A, m5C, and m1A associated with hepatocellular carcinoma and hope this review might provide therapeutic potent of RNA methylation to clinical research.

scholarly journals Involvement of Long Non-Coding RNAs (lncRNAs) in Tumor Angiogenesis

2020 ◽  
Vol 6 (4) ◽  
pp. 42 ◽  
Author(s):  
Julia Teppan ◽  
Dominik A. Barth ◽  
Felix Prinz ◽  
Katharina Jonas ◽  
Martin Pichler ◽  
...  
Keyword(s):  
Tumor Angiogenesis ◽  
Biological Processes ◽  
Protein Coding ◽  
Diagnostic Biomarkers ◽  
Oncogenic Pathways ◽  
Therapeutic Molecules ◽  
Cancer Types ◽  
Non Coding Rnas ◽  
Effective Use ◽  
To Receive

Long non-coding RNAs (lncRNAs) are defined as non-protein coding transcripts with a minimal length of 200 nucleotides. They are involved in various biological processes such as cell differentiation, apoptosis, as well as in pathophysiological processes. Numerous studies considered that frequently deregulated lncRNAs contribute to all hallmarks of cancer including metastasis, drug resistance, and angiogenesis. Angiogenesis, the formation of new blood vessels, is crucial for a tumor to receive sufficient amounts of nutrients and oxygen and therefore, to grow and exceed in its size over the diameter of 2 mm. In this review, the regulatory mechanisms of lncRNAs are described, which influence tumor angiogenesis by directly or indirectly regulating oncogenic pathways, interacting with other transcripts such as microRNAs (miRNAs) or modulating the tumor microenvironment. Further, angiogenic lncRNAs occurring in several cancer types such as liver, gastrointestinal cancer, or brain tumors are summarized. Growing evidence on the influence of lncRNAs on tumor angiogenesis verified these transcripts as potential predictive or diagnostic biomarkers or therapeutic targets of anti-angiogenesis treatment. However, there are many unsolved questions left which are pointed out in this review, hence driving comprehensive research in this area is necessary to enable an effective use of lncRNAs as either therapeutic molecules or diagnostic targets in cancer.

scholarly journals Long Non-Coding RNAs and Related Molecular Pathways in the Pathogenesis of Epilepsy

2019 ◽  
Vol 20 (19) ◽  
pp. 4898 ◽  
Author(s):  
Villa ◽  
Lavitrano ◽  
Combi
Keyword(s):  
Biological Processes ◽  
Complete Understanding ◽  
Aberrant Expression ◽  
Protein Coding ◽  
Diagnostic Biomarkers ◽  
Functional Roles ◽  
The Central Nervous System ◽  
Non Coding Rnas ◽  
Underlying Mechanisms ◽  
Coding Capacity

Epilepsy represents one of the most common neurological disorders characterized by abnormal electrical activity in the central nervous system (CNS). Recurrent seizures are the cardinal clinical manifestation. Although it has been reported that the underlying pathological processes include inflammation, changes in synaptic strength, apoptosis, and ion channels dysfunction, currently the pathogenesis of epilepsy is not yet completely understood. Long non-coding RNAs (lncRNAs), a class of long transcripts without protein-coding capacity, have emerged as regulatory molecules that are involved in a wide variety of biological processes. A growing number of studies reported that lncRNAs participate in the regulation of pathological processes of epilepsy and they are dysregulated during epileptogenesis. Moreover, an aberrant expression of lncRNAs linked to epilepsy has been observed both in patients and in animal models. In this review, we summarize latest advances concerning the mechanisms of action and the involvement of the most dysregulated lncRNAs in epilepsy. However, the functional roles of lncRNAs in the disease pathogenesis are still to be explored and we are only at the beginning. Additional studies are needed for the complete understanding of the underlying mechanisms and they would result in the use of lncRNAs as diagnostic biomarkers and novel therapeutic targets.

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